gpgraph-v2 1.0.0__tar.gz

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gpgraph_v2-1.0.0/Cargo.toml

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+[workspace]
+members = ["crates/gpgraph-core"]
+resolver = "2"
+
+[workspace.package]
+version = "1.0.0"
+edition = "2021"
+rust-version = "1.75"
+license = "MIT"
+authors = ["Luis Perez"]

gpgraph_v2-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Luis Perez
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

gpgraph_v2-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: gpgraph-v2
+Version: 1.0.0
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Rust
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Dist: numpy>=2.0
+Requires-Dist: networkx>=3.6
+Requires-Dist: gpmap-v2>=1.0
+Requires-Dist: tqdm>=4.67
+Requires-Dist: typing-extensions>=4.12
+Requires-Dist: matplotlib>=3.10 ; extra == 'plot'
+Requires-Dist: streamlit>=1.56 ; extra == 'streamlit'
+Requires-Dist: matplotlib>=3.10 ; extra == 'streamlit'
+Provides-Extra: plot
+Provides-Extra: streamlit
+License-File: LICENSE
+Summary: NetworkX-backed, Rust-accelerated graphs over genotype-phenotype maps.
+Keywords: genotype,phenotype,epistasis,fitness-landscape,networkx,graph
+Author-email: Luis Perez <lperezmo@users.noreply.github.com>
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Homepage, https://github.com/lperezmo/gpgraph-v2
+Project-URL: Issues, https://github.com/lperezmo/gpgraph-v2/issues
+Project-URL: Repository, https://github.com/lperezmo/gpgraph-v2
+
+# gpgraph-v2
+
+[![CI](https://github.com/lperezmo/gpgraph-v2/actions/workflows/ci.yml/badge.svg)](https://github.com/lperezmo/gpgraph-v2/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/gpgraph-v2.svg)](https://pypi.org/project/gpgraph-v2/)
+[![Python](https://img.shields.io/pypi/pyversions/gpgraph-v2.svg)](https://pypi.org/project/gpgraph-v2/)
+[![License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)
+[![Open in Streamlit](https://static.streamlit.io/badges/streamlit_badge_black_white.svg)](https://gpgraph-v2.streamlit.app)
+
+NetworkX-backed, Rust-accelerated graphs over genotype-phenotype maps.
+
+gpgraph-v2 lifts a [gpmap-v2](https://github.com/lperezmo/gpmap-v2) `GenotypePhenotypeMap` into a
+NetworkX `DiGraph`. Nodes carry the row attributes from the map; edges connect neighbors under
+a chosen distance metric (Hamming or codon). Fixation models (SSWM, ratio, Moran, McCandlish)
+populate an edge `prob` attribute for evolutionary trajectory analysis.
+
+This is a clean-break rewrite of [harmslab/gpgraph](https://github.com/harmslab/gpgraph).
+Hot paths live in Rust via PyO3 + rayon; fixation models stay in vectorized numpy.
+
+## Why v2
+
+- **Fast.** Neighbor detection runs in Rust with rayon parallelism. Biallelic cutoff-1 and
+  cutoff-2 hit a bit-flip fast path: `O(N * L^cutoff)` instead of `O(N^2 * L)`.
+- **Typed.** Full type hints, `mypy --strict` in CI.
+- **Modern tooling.** `uv` + `maturin` + `pyproject.toml`. Releases via
+  `python-semantic-release`. OIDC-based PyPI publishing.
+- **Consumes gpmap-v2.** Speaks the locked `SCHEMA.md` contract; reads `binary_packed`,
+  `n_mutations`, and `phenotypes` (not the removed v1 `fitnesses`).
+- **No Cython, no `setup.py`, no `.c` blobs.**
+
+## Install
+
+```bash
+pip install gpgraph-v2
+```
+
+Or with uv:
+
+```bash
+uv add gpgraph-v2
+```
+
+Plotting support is optional. For matplotlib:
+
+```bash
+pip install "gpgraph-v2[plot]"
+```
+
+Python 3.11+. Prebuilt wheels ship for Linux (x86_64, aarch64), macOS (x86_64, aarch64),
+and Windows (x64).
+
+## Quick start
+
+```python
+from gpmap import GenotypePhenotypeMap
+from gpgraph import GenotypePhenotypeGraph
+
+gpm = GenotypePhenotypeMap(
+    wildtype="AAA",
+    genotypes=["AAA", "AAT", "ATA", "TAA", "ATT", "TAT", "TTA", "TTT"],
+    phenotypes=[0.1, 0.2, 0.2, 0.6, 0.4, 0.6, 1.0, 1.1],
+    stdeviations=[0.05] * 8,
+)
+
+G = GenotypePhenotypeGraph.from_gpm(gpm)
+G.number_of_nodes()  # 8
+G.number_of_edges()  # 24 directed (12 undirected pairs)
+
+G.add_model(column="phenotypes", model="sswm")
+G.edges[(0, 1)]["prob"]  # SSWM fixation probability from AAA -> AAT
+```
+
+Available fixation models: `"sswm"`, `"ratio"`, `"moran"`, `"mcclandish"`. Pass
+`population_size=N` as a keyword for the last two. Pass any `f(fi, fj, **kw) -> float`
+for a custom model.
+
+## Forward paths and flux
+
+```python
+from gpgraph.paths import forward_paths_prob, paths_prob_to_edges_flux
+
+G.add_model(column="phenotypes", model="sswm")
+paths = forward_paths_prob(G, source=0, target=7)
+flux = paths_prob_to_edges_flux(paths)
+```
+
+## Plotting
+
+```python
+from gpgraph.pyplot import draw_gpgraph, draw_paths
+
+fig, ax = draw_gpgraph(G)             # Hamming-weight vertical layout
+draw_paths(G, source=0, target=7)     # paths flux overlay
+```
+
+## Benchmarks
+
+Rust kernels vs a pure-Python pairwise reference. Windows 11, Ryzen, release build.
+Run via `uv run pytest tests/benchmarks/ --benchmark-only`.
+
+| problem              | bit-flip (Rust) | pairwise (Rust) | pairwise (Python) |
+|---|---|---|---|
+| N=256, L=6, cutoff=1 | 77 us           | 284 us          | 29.3 ms           |
+| N=1024, L=8, cutoff=1| 167 us          | 1.2 ms          | (skipped, minutes)|
+
+At L=6 the Rust bit-flip path is ~380x faster than a naive Python loop. Past
+N = 1000 on biallelic data the bit-flip specialization pulls away from the
+rayon-parallel pairwise version by another ~7x.
+
+## Dispatch policy (neighbor kernels)
+
+`gpgraph.neighbors.get_neighbors` chooses the fastest available implementation:
+
+| problem shape                                     | kernel |
+|---|---|
+| user-supplied `f(g1, g2, cutoff=...) -> bool`     | pure Python `O(N^2)` |
+| Hamming, biallelic `binary_packed`, cutoff <= 2   | Rust bit-flip (`O(N * C(L, cutoff))`) |
+| Hamming, biallelic `binary_packed`, larger cutoff | Rust rayon-parallel packed pairwise |
+| Hamming, non-binary alphabet                      | Rust rayon-parallel string pairwise |
+| codon                                             | Rust rayon-parallel codon pairwise |
+
+See [SCHEMA.md](SCHEMA.md) for the full node/edge contract.
+
+## Development
+
+```bash
+git clone https://github.com/lperezmo/gpgraph-v2
+cd gpgraph-v2
+uv sync
+uv run maturin develop --release
+uv run pytest
+uv run ruff check python/gpgraph tests
+```
+
+After editing Rust:
+
+```bash
+uv run maturin develop --release && uv run pytest
+```
+
+## Consuming from another local project
+
+During co-development with gpmap-v2, point at the local source:
+
+```toml
+[tool.uv.sources]
+gpgraph-v2 = { path = "/absolute/path/to/gpgraph-v2", editable = true }
+
+[project]
+dependencies = ["gpgraph-v2"]
+```
+
+Imports remain `from gpgraph import GenotypePhenotypeGraph`.
+
+## Migration from v1 (`harmslab/gpgraph`)
+
+gpgraph-v2 is not wire-compatible with v1. Key differences:
+
+- Distribution name is `gpgraph-v2` on PyPI; import path is still `gpgraph`.
+- Construction: use `GenotypePhenotypeGraph.from_gpm(gpm, ...)`. The v1 two-step
+  `G = GenotypePhenotypeGraph(); G.add_gpm(gpm)` is removed.
+- Reads gpmap-v2 columns: node attribute is `phenotypes`, not `fitnesses`.
+- `__repr__` no longer renders a matplotlib figure as a side effect.
+- Matplotlib is an optional extra (`gpgraph-v2[plot]`); the core install is headless.
+- The `_nx_wrapper` introspection shim in `pyplot/primitives.py` is gone. NetworkX is
+  version-pinned to `>=3.6`.
+- `gpgraph.neighbor_functions` is renamed `gpgraph.neighbors` and the pairwise
+  `get_neighbors` returns a NumPy `(E, 2) int64` array instead of a list of tuples.
+- Python 3.11+.
+
+## Releases
+
+Releases are driven by [`python-semantic-release`](https://python-semantic-release.readthedocs.io/)
+on merge to `main`. Commits follow [Conventional Commits](https://www.conventionalcommits.org/):
+
+- `fix: ...` -> patch
+- `feat: ...` -> minor
+- `feat!: ...` or a `BREAKING CHANGE:` footer -> major
+
+`CHANGELOG.md`, version bumps, Git tags, GitHub Releases, wheel builds, and PyPI uploads
+all happen automatically.
+
+## License
+
+MIT. See [LICENSE](LICENSE).
+